Python script for six frame translation of sequences !
from Bio import SeqIO from Bio.Seq import Seq def translate_frame(sequence, frame): if frame > 0: translated_seq = sequence[frame-1:].translate() else:...ord in records: print(f"Sequence ID: {record.id}") fo...s(frame)} Translation:\n{protein_sequence...146 days ago
Raku script to find repeats in sequences !
sub find-repeats($sequence, $min-repeat-length = 3) { my @repeats; for ^($sequence.chars - $min-repeat-length + 1) -> $i { my $substring = $sequence.substr($i, $min-repeat-length...peats; } # Example usage my $genome-sequence...146 days ago
Python script to find repeats in the DNA sequence !
def find_repeats(sequence, min_repeat_length=3): repeats = [] for i in range(len(sequence) - min_repeat_length + 1): substring = sequence[i:i+min_repeat_length] if s...return repeats # Example usage genome_sequence...146 days ago
Raku script to find microsatellites in DNA fragments !
sub find-microsatellites($sequence, $min-repeat-length = 2, $max-repeat-len...max-repeat-length) { for ^($sequence.chars - $repeat-length * $min...> $i { my $substring = $sequence.substr($i, $repeat-length);...esult = find-microsatellites($genome-sequence...146 days ago
Perl script to calculate the basic stats of the assembled genome !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; # Input file containing the genome assembly in FASTA...gth = 0; my $num_contigs = 0; my @contig_lengths; # Iterate through each sequence...146 days ago
Python script for basic stats of the assembled genome !
from Bio import SeqIO import statistics # Input file containing the genome assembly in FASTA format input_file...al_length = 0 num_contigs = 0 contig_lengths = [] # Iterate through each sequence...146 days ago
Python script to convert fastq to fasta
def fastq_to_fasta(fastq_file, fasta_file): with open(fastq_file, 'r') as fq:...header = fq.readline().strip() sequence = fq.readline().strip()...'>' + header[1:] + '\n') fa.write(sequence...91 days ago
Python script to finds extact similar sequence between two multi fasta files !
from Bio.Blast.Applications import NcbiblastnCommandline import os import sys def perform_local_bl...'\t') qseq = fields[0] # Extract the aligned query sequence (qseq) #print("Aligned Query Sequence...55 days ago
Python script to create fastq file with random sequences
import random def generate_random_sequence(length): bases = ['A', 'C', 'G', '...ge(length)) def generate_fastq_entry(sequence_length): sequence = generate_random_sequence(sequence_length) quality = genera...FASTQ file with 5 entries, each with a sequence...16 days ago
Python script to calculate basic genome stats !
from Bio import SeqIO def calculate_genome_stats(fasta_file): # Initialize variab...ount = 0 g_count = 0 # Read the genome sequence from the FASTA file for...cord in SeqIO.parse(fasta_file, "fasta"): sequence...16 days ago